Correlation does not equal causation
NSA articles may be more often penalized...but they are likely more often to be flagged. It's not that people here are defending the NSA or anything, it's that people have often said that they are tired of reading NSA all the time. And so, their reaction may be to flag those stories, giving them a penalty.
The referenced article does not really account for that, AFAIK
Edit: Several people said I should have said more in the article about flagging. There's no way to distinguish between penalties applied by administrators and penalties due to flagging. So there's not much I can say.